Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

tag_button

FMODB ID: 5NNQZ

Calculation Name: 5DQS-A-Xray372

Preferred Name: Elongation factor 1-beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5DQS

Chain ID: A

ChEMBL ID: CHEMBL4295731

UniProt ID: P24534

Base Structure: X-ray

Registration Date: 2023-09-27

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2555319.627533
FMO2-HF: Nuclear repulsion 2470899.129178
FMO2-HF: Total energy -84420.498354
FMO2-MP2: Total energy -84668.209762


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:0:ALA)


Summations of interaction energy for fragment #1(A:0:ALA)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-1.8550.082999999999999-0.011-1.17-0.7570.006
Interaction energy analysis for fragmet #1(A:0:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / q_NPA : 0.018
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A2ALA0-0.0030.0043.845-2.190-0.252-0.011-1.170-0.7570.006
4A3ALA00.0480.0226.2130.3910.3910.0000.0000.0000.000
5A4GLY00.0360.0318.0990.0780.0780.0000.0000.0000.000
6A5THR0-0.052-0.01711.6460.0830.0830.0000.0000.0000.000
7A6LEU0-0.027-0.01415.322-0.015-0.0150.0000.0000.0000.000
8A7TYR0-0.046-0.02717.4320.0580.0580.0000.0000.0000.000
9A8THR00.030-0.02721.023-0.005-0.0050.0000.0000.0000.000
10A9TYR00.0130.02623.6350.0070.0070.0000.0000.0000.000
11A10PRO00.034-0.01226.063-0.015-0.0150.0000.0000.0000.000
12A11GLU-1-0.889-0.94026.488-0.188-0.1880.0000.0000.0000.000
13A12ASN0-0.0120.00524.6360.0170.0170.0000.0000.0000.000
14A13TRP00.0570.01824.396-0.025-0.0250.0000.0000.0000.000
15A14ARG10.8650.92023.6530.2020.2020.0000.0000.0000.000
16A15ALA00.000-0.00120.596-0.031-0.0310.0000.0000.0000.000
17A16PHE00.0250.00519.579-0.038-0.0380.0000.0000.0000.000
18A17LYS10.8890.95819.5910.2820.2820.0000.0000.0000.000
19A18ALA00.012-0.00215.527-0.025-0.0250.0000.0000.0000.000
20A19LEU0-0.0040.00114.939-0.067-0.0670.0000.0000.0000.000
21A20ILE00.0210.00515.958-0.008-0.0080.0000.0000.0000.000
22A21ALA0-0.002-0.00713.5680.0120.0120.0000.0000.0000.000
23A22ALA00.0140.00911.150-0.033-0.0330.0000.0000.0000.000
24A23GLN0-0.049-0.01011.2260.0250.0250.0000.0000.0000.000
25A24TYR0-0.019-0.01812.5110.0600.0600.0000.0000.0000.000
26A25SER0-0.046-0.0307.6540.0680.0680.0000.0000.0000.000
27A26GLY00.0420.0257.0370.0270.0270.0000.0000.0000.000
28A27ALA0-0.030-0.0057.143-0.095-0.0950.0000.0000.0000.000
29A28GLN0-0.040-0.0305.5320.3030.3030.0000.0000.0000.000
30A29VAL0-0.011-0.00810.091-0.048-0.0480.0000.0000.0000.000
31A30ARG10.8500.90812.9990.6520.6520.0000.0000.0000.000
32A31VAL00.0430.01915.895-0.018-0.0180.0000.0000.0000.000
33A32LEU0-0.041-0.01219.2620.0360.0360.0000.0000.0000.000
34A33SER00.033-0.01021.9430.0010.0010.0000.0000.0000.000
35A34ALA00.0590.02325.1670.0120.0120.0000.0000.0000.000
36A35PRO0-0.045-0.01124.4170.0060.0060.0000.0000.0000.000
37A36PRO00.0090.00124.9760.0110.0110.0000.0000.0000.000
38A37HIS00.0050.01027.9260.0050.0050.0000.0000.0000.000
39A38PHE0-0.026-0.02031.1220.0070.0070.0000.0000.0000.000
40A39HIS00.021-0.01025.8910.0080.0080.0000.0000.0000.000
41A40PHE0-0.0180.00424.387-0.022-0.0220.0000.0000.0000.000
42A41GLY00.0460.02527.9880.0130.0130.0000.0000.0000.000
43A42GLN0-0.013-0.01330.370-0.004-0.0040.0000.0000.0000.000
44A43THR00.0510.02526.5800.0080.0080.0000.0000.0000.000
45A44ASN0-0.016-0.00326.8730.0050.0050.0000.0000.0000.000
46A45ARG10.8630.93127.8660.1660.1660.0000.0000.0000.000
47A46THR0-0.0090.01027.8100.0080.0080.0000.0000.0000.000
48A47PRO00.0620.00828.647-0.010-0.0100.0000.0000.0000.000
49A48GLU-1-0.763-0.85722.885-0.221-0.2210.0000.0000.0000.000
50A49PHE0-0.0310.00023.061-0.020-0.0200.0000.0000.0000.000
51A50LEU00.0160.00324.285-0.014-0.0140.0000.0000.0000.000
52A51ARG10.8220.90421.3080.2100.2100.0000.0000.0000.000
53A52LYS10.8100.90519.1990.3010.3010.0000.0000.0000.000
54A53PHE0-0.010-0.03417.792-0.026-0.0260.0000.0000.0000.000
55A54PRO00.0380.03422.7460.0160.0160.0000.0000.0000.000
56A55ALA0-0.030-0.01225.0560.0140.0140.0000.0000.0000.000
57A56GLY0-0.0050.01326.2040.0130.0130.0000.0000.0000.000
58A57LYS10.8140.88423.2510.2780.2780.0000.0000.0000.000
59A58VAL00.0050.03923.513-0.012-0.0120.0000.0000.0000.000
60A59PRO0-0.078-0.06320.2070.0210.0210.0000.0000.0000.000
61A60ALA0-0.036-0.01519.5400.0050.0050.0000.0000.0000.000
62A61PHE00.008-0.00110.4190.0150.0150.0000.0000.0000.000
63A62GLU-1-0.746-0.86314.911-0.354-0.3540.0000.0000.0000.000
64A63GLY00.0070.00610.706-0.021-0.0210.0000.0000.0000.000
65A64ASP-1-0.817-0.9259.428-0.627-0.6270.0000.0000.0000.000
66A65ASP-1-0.908-0.9518.359-1.027-1.0270.0000.0000.0000.000
67A66GLY0-0.010-0.00210.9540.1020.1020.0000.0000.0000.000
68A67PHE0-0.046-0.00210.7600.0720.0720.0000.0000.0000.000
69A68CYS0-0.045-0.01912.795-0.035-0.0350.0000.0000.0000.000
70A69VAL0-0.006-0.00213.7490.0300.0300.0000.0000.0000.000
71A70PHE00.0350.00516.456-0.001-0.0010.0000.0000.0000.000
72A71GLU-1-0.728-0.83519.167-0.241-0.2410.0000.0000.0000.000
73A72SER0-0.037-0.03919.003-0.038-0.0380.0000.0000.0000.000
74A73ASN00.015-0.00718.746-0.047-0.0470.0000.0000.0000.000
75A74ALA00.0090.01116.710-0.035-0.0350.0000.0000.0000.000
76A75ILE00.0040.00714.560-0.089-0.0890.0000.0000.0000.000
77A76ALA00.0310.01313.664-0.115-0.1150.0000.0000.0000.000
78A77TYR00.0500.03712.184-0.085-0.0850.0000.0000.0000.000
79A78TYR00.0160.0127.848-0.177-0.1770.0000.0000.0000.000
80A79VAL0-0.022-0.0058.950-0.372-0.3720.0000.0000.0000.000
81A80SER0-0.0040.0029.7800.0720.0720.0000.0000.0000.000
82A81ASN00.003-0.0197.993-0.339-0.3390.0000.0000.0000.000
83A82GLU-1-0.933-0.9749.040-0.035-0.0350.0000.0000.0000.000
84A83GLU-1-0.875-0.93110.837-0.130-0.1300.0000.0000.0000.000
85A84LEU0-0.057-0.01512.6080.0280.0280.0000.0000.0000.000
86A85ARG10.8490.9177.2161.3271.3270.0000.0000.0000.000
87A86GLY00.0030.00514.4160.0340.0340.0000.0000.0000.000
88A87SER00.0180.00614.503-0.016-0.0160.0000.0000.0000.000
89A88THR0-0.023-0.01915.5180.0210.0210.0000.0000.0000.000
90A89PRO00.0600.02018.650-0.027-0.0270.0000.0000.0000.000
91A90GLU-1-0.839-0.90520.274-0.080-0.0800.0000.0000.0000.000
92A91ALA0-0.009-0.00419.094-0.010-0.0100.0000.0000.0000.000
93A92ALA00.0220.01017.288-0.018-0.0180.0000.0000.0000.000
94A93ALA0-0.018-0.00819.008-0.018-0.0180.0000.0000.0000.000
95A94GLN0-0.002-0.01422.476-0.005-0.0050.0000.0000.0000.000
96A95VAL0-0.0030.00417.8150.0010.0010.0000.0000.0000.000
97A96VAL00.0160.00619.998-0.006-0.0060.0000.0000.0000.000
98A97GLN0-0.0160.01822.1800.0110.0110.0000.0000.0000.000
99A98TRP00.011-0.00424.2160.0070.0070.0000.0000.0000.000
100A99VAL0-0.026-0.00720.4280.0010.0010.0000.0000.0000.000
101A100SER0-0.024-0.03223.8950.0000.0000.0000.0000.0000.000
102A101PHE00.0040.01526.4830.0090.0090.0000.0000.0000.000
103A102ALA00.000-0.01126.2120.0090.0090.0000.0000.0000.000
104A103ASP-1-0.842-0.93125.358-0.223-0.2230.0000.0000.0000.000
105A104SER0-0.027-0.01928.5040.0040.0040.0000.0000.0000.000
106A105ASP-1-0.824-0.90431.641-0.103-0.1030.0000.0000.0000.000
107A106ILE0-0.033-0.01229.8240.0070.0070.0000.0000.0000.000
108A107VAL0-0.014-0.00629.0010.0040.0040.0000.0000.0000.000
109A108PRO00.0180.03232.2270.0040.0040.0000.0000.0000.000
110A109PRO00.0340.02935.4770.0040.0040.0000.0000.0000.000
111A110ALA00.0550.01634.1230.0060.0060.0000.0000.0000.000
112A111SER0-0.040-0.02834.3410.0000.0000.0000.0000.0000.000
113A112THR0-0.067-0.03536.5640.0050.0050.0000.0000.0000.000
114A113TRP00.002-0.00939.7280.0050.0050.0000.0000.0000.000
115A114VAL00.015-0.00436.0620.0030.0030.0000.0000.0000.000
116A115PHE00.0320.01333.8790.0010.0010.0000.0000.0000.000
117A116PRO00.0110.01839.4730.0020.0020.0000.0000.0000.000
118A117THR0-0.110-0.04440.4070.0020.0020.0000.0000.0000.000
119A118LEU0-0.033-0.02636.1170.0000.0000.0000.0000.0000.000
120A119GLY00.0310.02940.6140.0010.0010.0000.0000.0000.000
121A120ILE0-0.089-0.04337.1890.0000.0000.0000.0000.0000.000
122A121MET0-0.019-0.01740.038-0.001-0.0010.0000.0000.0000.000
123A122HIS00.0260.02642.5430.0010.0010.0000.0000.0000.000
124A123HIS00.0530.03345.899-0.003-0.0030.0000.0000.0000.000
125A124ASN00.0350.01947.2090.0050.0050.0000.0000.0000.000
126A125LYS10.8750.91648.4450.0570.0570.0000.0000.0000.000
127A126GLN00.0480.03649.847-0.001-0.0010.0000.0000.0000.000
128A127ALA00.0480.03445.292-0.001-0.0010.0000.0000.0000.000
129A128THR00.003-0.02644.394-0.003-0.0030.0000.0000.0000.000
130A129GLU-1-0.767-0.86644.778-0.065-0.0650.0000.0000.0000.000
131A130ASN0-0.025-0.03045.7240.0000.0000.0000.0000.0000.000
132A131ALA00.0080.00941.037-0.002-0.0020.0000.0000.0000.000
133A132LYS10.8290.90941.1160.0640.0640.0000.0000.0000.000
134A133GLU-1-0.885-0.94742.257-0.064-0.0640.0000.0000.0000.000
135A134GLU-1-0.805-0.86839.126-0.089-0.0890.0000.0000.0000.000
136A135VAL0-0.010-0.00937.022-0.003-0.0030.0000.0000.0000.000
137A136ARG10.8410.93738.2220.0650.0650.0000.0000.0000.000
138A137ARG10.7690.84936.6520.0930.0930.0000.0000.0000.000
139A138ILE0-0.008-0.00133.721-0.001-0.0010.0000.0000.0000.000
140A139LEU0-0.024-0.01034.626-0.002-0.0020.0000.0000.0000.000
141A140GLY00.027-0.00636.3980.0010.0010.0000.0000.0000.000
142A141LEU0-0.044-0.00933.2630.0030.0030.0000.0000.0000.000
143A142LEU00.013-0.00130.1300.0000.0000.0000.0000.0000.000
144A143ASP-1-0.784-0.87833.293-0.066-0.0660.0000.0000.0000.000
145A144ALA0-0.021-0.02435.7370.0040.0040.0000.0000.0000.000
146A145TYR0-0.036-0.00427.5730.0070.0070.0000.0000.0000.000
147A146LEU00.0180.00328.4960.0020.0020.0000.0000.0000.000
148A147LYS10.8400.94332.2230.0620.0620.0000.0000.0000.000
149A148THR0-0.032-0.02433.6810.0020.0020.0000.0000.0000.000
150A149ARG10.9270.97828.3600.0790.0790.0000.0000.0000.000
151A150THR0-0.0160.00226.2150.0010.0010.0000.0000.0000.000
152A151PHE0-0.008-0.02623.218-0.008-0.0080.0000.0000.0000.000
153A152LEU0-0.041-0.02624.3230.0100.0100.0000.0000.0000.000
154A153VAL0-0.005-0.00521.0900.0100.0100.0000.0000.0000.000
155A154GLY00.0150.01721.861-0.005-0.0050.0000.0000.0000.000
156A155GLU-1-0.846-0.92822.166-0.069-0.0690.0000.0000.0000.000
157A156ARG10.8630.92818.1450.0720.0720.0000.0000.0000.000
158A157VAL00.0240.03317.984-0.005-0.0050.0000.0000.0000.000
159A158THR00.0200.01517.088-0.020-0.0200.0000.0000.0000.000
160A159LEU00.021-0.01214.5260.0040.0040.0000.0000.0000.000
161A160ALA00.0050.02518.2680.0090.0090.0000.0000.0000.000
162A161ASP-1-0.722-0.87421.616-0.164-0.1640.0000.0000.0000.000
163A162ILE00.0230.01816.8130.0090.0090.0000.0000.0000.000
164A163THR00.000-0.00820.580-0.004-0.0040.0000.0000.0000.000
165A164VAL00.0090.01722.6780.0130.0130.0000.0000.0000.000
166A165VAL0-0.0050.00624.3380.0130.0130.0000.0000.0000.000
167A166CYS0-0.048-0.02922.6530.0070.0070.0000.0000.0000.000
168A167THR0-0.047-0.04125.5800.0050.0050.0000.0000.0000.000
169A168LEU0-0.035-0.01428.0960.0130.0130.0000.0000.0000.000
170A169LEU0-0.0090.01126.8050.0120.0120.0000.0000.0000.000
171A170TRP00.052-0.00229.9440.0140.0140.0000.0000.0000.000
172A171LEU00.0370.02732.9740.0080.0080.0000.0000.0000.000
173A172TYR00.012-0.02032.1290.0080.0080.0000.0000.0000.000
174A173LYS10.9140.98931.0590.1450.1450.0000.0000.0000.000
175A174GLN0-0.028-0.02035.1260.0020.0020.0000.0000.0000.000
176A175VAL00.027-0.00738.0250.0060.0060.0000.0000.0000.000
177A176LEU0-0.0130.02035.5570.0050.0050.0000.0000.0000.000
178A177GLU-1-0.720-0.83239.327-0.061-0.0610.0000.0000.0000.000
179A178PRO0-0.020-0.01241.7300.0000.0000.0000.0000.0000.000
180A179SER0-0.032-0.02742.7390.0000.0000.0000.0000.0000.000
181A180PHE00.0100.00940.6560.0020.0020.0000.0000.0000.000
182A181ARG10.9020.92937.6180.0770.0770.0000.0000.0000.000
183A182GLN0-0.0160.00539.8750.0000.0000.0000.0000.0000.000
184A183ALA0-0.040-0.01342.4290.0020.0020.0000.0000.0000.000
185A184PHE0-0.0140.00237.5830.0000.0000.0000.0000.0000.000
186A185PRO00.0290.01937.350-0.005-0.0050.0000.0000.0000.000
187A186ASN0-0.009-0.02634.4800.0000.0000.0000.0000.0000.000
188A187THR00.0380.02032.310-0.004-0.0040.0000.0000.0000.000
189A188ASN00.0270.01332.074-0.012-0.0120.0000.0000.0000.000
190A189ARG10.8710.93430.5090.0720.0720.0000.0000.0000.000
191A190TRP0-0.036-0.00625.662-0.001-0.0010.0000.0000.0000.000
192A191PHE00.0220.01127.983-0.009-0.0090.0000.0000.0000.000
193A192LEU0-0.010-0.01428.356-0.007-0.0070.0000.0000.0000.000
194A193THR00.003-0.01025.8050.0000.0000.0000.0000.0000.000
195A194CYS0-0.022-0.00324.102-0.006-0.0060.0000.0000.0000.000
196A195ILE0-0.042-0.02023.671-0.011-0.0110.0000.0000.0000.000
197A196ASN0-0.056-0.03625.5320.0000.0000.0000.0000.0000.000
198A197GLN0-0.079-0.02220.7220.0110.0110.0000.0000.0000.000
199A198PRO00.0280.00219.385-0.012-0.0120.0000.0000.0000.000
200A199GLN00.0500.02015.1800.0100.0100.0000.0000.0000.000
201A200PHE00.0290.00418.302-0.027-0.0270.0000.0000.0000.000
202A201ARG10.8540.91021.1060.1050.1050.0000.0000.0000.000
203A202ALA0-0.0120.00219.1460.0070.0070.0000.0000.0000.000
204A203VAL0-0.057-0.02218.741-0.013-0.0130.0000.0000.0000.000
205A204LEU0-0.056-0.03121.7440.0090.0090.0000.0000.0000.000
206A205GLY00.0230.03124.8790.0110.0110.0000.0000.0000.000
207A206GLU-1-0.874-0.92326.856-0.098-0.0980.0000.0000.0000.000
208A207VAL0-0.015-0.00328.230-0.002-0.0020.0000.0000.0000.000
209A208LYS10.8250.89631.0790.0810.0810.0000.0000.0000.000
210A209LEU0-0.015-0.01933.036-0.002-0.0020.0000.0000.0000.000
211A210CYS0-0.0320.01836.2300.0060.0060.0000.0000.0000.000
212A211GLU-1-0.795-0.88639.140-0.067-0.0670.0000.0000.0000.000
213A212LYS10.8380.89042.3020.0620.0620.0000.0000.0000.000
214A213MET0-0.031-0.02443.153-0.003-0.0030.0000.0000.0000.000
215A214ALA0-0.0020.02141.8140.0030.0030.0000.0000.0000.000